Lecture 14

Question 1

Common Features of globular proteins

Answer 1

• Charged polar residues (Arg, His, Lys, Asp, Glu) are usually found on the surface of a protein where they favor solubility by forming hydrogen bonds to water
• Uncharged polar residues (Ser, Thr, Asp, Gln, Tyr, Trp) Tend to be on the surface of a protein but also occur on the interior forming hydrogen bonds with other groups
• Non-polar residues (val, Leu, Ile, Met, Phe) prefer the interior of a protein where they avoid contact with the aqueous solvent

Question 2

Salt Bridges

Answer 2

• occur when folding
• particularly favorable interaction that combines a hydrogen bond and an electrostatic attraction
• hydrogen bond acceptor is usually one of the carboxylate residues (glu or asp). The most common donors are the protonated side chains of lys, arg, and his

Question 3

thiols oxidize to what?

Answer 3

Thiols are oxidized under mild conditions to give disulfides; the reverse reaction works as well
2R-SH—>R-S-S-R

Question 4

why are disulfides important?

Answer 4

Disulfides are important because nearby cys residues can form disulfides that cross-link the polypeptide chain

Question 5

epidermal growth factor

Answer 5

Small signaling protein that has 3 disulfide linkages

-The protein binds to a receptor on the surface of the cell to “turn on” cell growth

Question 6

Thermodynamics of protein folding

Answer 6

1) Entropy of folding
- Protein becomes ordered in the folding process
2) Hydrophobic effect
- entropy affect favors folding (ordered water molecules)
3) Enthalpy of folding
- internal H-bonds
- dispersion forces
- salt bridges
- disulfide linkages

Question 7

Entropy of solvation

Answer 7

Folding tends to place the hydrophobic residues inside the protein, away from aqueous solvent
-hydrophobic residue on the surface of a protein must be enclosed by an ordered case of water molecules; folding releases the ordered water molecules and increases the entropy of the system

Question 8

multiple subunits

Answer 8

• With single polypeptide chains, organization stops at the tertiary structure
• If there are multiple polypeptides, there are subunits and are arranged in the quaternary structure

Question 9

Subunit symmetry

Answer 9

Simplest quaternary structures place 2 or 3 subunits in a symmetrical arrangement

Question 10

homotypic protein

Answer 10

all subunits are the same

Question 11

heterotypic protein

Answer 11

subunits are not all the same

Question 12

Catalyst

Answer 12

Substance that increases the rate of a chemical reaction, even though the catalyst is not part of the stoichiometry of the reaction, nor is it changed or consumed by the reaction

Question 13

common catalysts

Answer 13

acid catalysts, base catalysts, nucleophilic catalyst, metal ion catalysts can increase the rate as much as 10^4
-in biological systems virtually all are catalyzed by enzymes; can be up to 10^18 as fast

Question 14

Acid Catalyst

Answer 14

Increases the rate of the reaction by protonating a reactant

Question 15

Specific Acid Catalysis

Answer 15

Proton transfer is complete before the start of the rate determining step

Question 16

Transesterification

Answer 16

converts one ester into another